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- PDB-9ve9: Hemoglobin amyloid fibril -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9ve9
TitleHemoglobin amyloid fibril
ComponentsHemoglobin subunit beta
KeywordsPROTEIN FIBRIL
Function / homology
Function and homology information


Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport ...Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / erythrocyte development / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
Hemoglobin subunit beta
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsLi, S. / Cao, Q. / Cao, Y.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)National Key R&D Program of China (2024YFF1106604) China
National Natural Science Foundation of China (NSFC)32271276 China
CitationJournal: To Be Published
Title: Structure of hemoglobin subunit beta (bovin) at 2.6 angstroms resolution
Authors: Li, S. / Cao, Q. / Cao, Y.
History
DepositionJun 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit beta
B: Hemoglobin subunit beta
C: Hemoglobin subunit beta
D: Hemoglobin subunit beta
E: Hemoglobin subunit beta
F: Hemoglobin subunit beta
G: Hemoglobin subunit beta
H: Hemoglobin subunit beta
I: Hemoglobin subunit beta
J: Hemoglobin subunit beta


Theoretical massNumber of molelcules
Total (without water)159,77410
Polymers159,77410
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15977.382 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02070
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Hemoglobin amyloid fibril / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 2
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2EPUimage acquisition
4CTFFINDCTF correction
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.5912 ° / Axial rise/subunit: 4.782 Å / Axial symmetry: C1
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31408 / Symmetry type: HELICAL

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